## [1] "O76_p4_IFNg_R1_2.hicup.bam"
Truncation & Mapping
Truncation Frequency
| Total |
64,133,961 |
64,133,961 |
| Not Truncated |
39,030,916 |
39,002,865 |
| Truncated |
25,103,045 |
25,131,096 |
Truncated Read Length
| Average Length Truncated |
47.6 |
45.5 |
Mapping Efficiency
| Too Short To Map |
3,949,166 |
4,046,436 |
| Unique Alignments |
55,068,279 |
54,066,564 |
| Multiple Alignments |
2,288,807 |
1,997,064 |
| Failed To Align |
2,827,709 |
4,023,897 |
| Paired |
47,066,050 |
47,066,050 |
Truncation and Mapping Bar Plot
Filtering
Filtering Breakdown by Category
| Valid Pairs |
26,549,206 |
| Invalid Pairs |
20,516,844 |
| Same Circularised |
584,200 |
| Same Dangling Ends |
3,759,715 |
| Same Fragment Internal |
9,041,643 |
| Re Ligation |
5,290,816 |
| Contiguous Sequence |
111,049 |
| Wrong Size |
1,729,421 |
| Total Pairs |
47,066,050 |
Filtering Breakdown Pie Chart
Ditag Length Distribution
Deduplication
Deduplication Summary Table
| Read Pairs |
26,549,206 |
38,541 |
| Cis-close (<10Kbp) |
3,446,749 |
4,190 |
| Cis-far (>10Kbp) |
15,839,281 |
21,264 |
| Trans |
7,263,176 |
13,087 |
Deduplication Bar Chart
Analysis produced by HiCUP - a tool for mapping and performing quality control on Hi-C data
